* using log directory 'd:/RCompile/CRANincoming/R-devel/rwty.Rcheck'
* using R version 4.5.0 alpha (2025-03-25 r88054 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'rwty/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rwty' version '1.0.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] NOTE
Maintainer: 'Dan Warren <dan.l.warren@gmail.com>'

Possibly misspelled words in DESCRIPTION:
  Lanfear (19:77)

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following \keyword or \concept entries
which likely give several index terms:
  File 'analyze.rwty.Rd':
    \keyword{MCMC,}
    \keyword{plots,}
    \keyword{rwty,}
    \keyword{topology,}
  File 'check.chains.Rd':
    \keyword{MCMC,}
    \keyword{awty,}
    \keyword{convergence,}
    \keyword{phylogenetics,}
  File 'clade.freq.Rd':
    \keyword{consensus,}
    \keyword{frequencies,}
    \keyword{mcmc,}
  File 'combine.ptables.Rd':
    \keyword{MCMC,}
    \keyword{awty,}
    \keyword{convergence,}
    \keyword{phylogenetics,}
  File 'cumulative.freq.Rd':
    \keyword{MCMC,}
    \keyword{frequency,}
  File 'estimate.autocorr.m.Rd':
    \keyword{autocorrelation,}
  File 'load.multi.Rd':
    \keyword{MCMC,}
    \keyword{Phylogenetics,}
    \keyword{load,}
  File 'load.trees.Rd':
    \keyword{MCMC,}
    \keyword{Phylogenetics,}
  File 'makeplot.acsf.cumulative.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{phylogenetics,}
  File 'makeplot.acsf.sliding.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{phylogenetics,}
  File 'makeplot.all.params.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{parameter,}
    \keyword{plot,}
  File 'makeplot.asdsf.Rd':
    \keyword{ASDSF,}
    \keyword{MCMC,}
    \keyword{phylogenetics,}
  File 'makeplot.autocorr.Rd':
    \keyword{autocorrelation,}
  File 'makeplot.pairs.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{parameter,}
    \keyword{plot,}
  File 'makeplot.param.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{parameter,}
    \keyword{plot,}
  File 'makeplot.pseudo.ess.Rd':
    \keyword{ESS,}
  File 'makeplot.splitfreq.matrix.Rd':
    \keyword{MCMC,}
    \keyword{consensus,}
    \keyword{convergence,}
    \keyword{frequency,}
    \keyword{phylogenetics,}
  File 'makeplot.splitfreqs.cumulative.Rd':
    \keyword{mcmc,}
    \keyword{phylogenetics,}
    \keyword{window,}
  File 'makeplot.splitfreqs.sliding.Rd':
    \keyword{mcmc,}
    \keyword{phylogenetics,}
    \keyword{window,}
  File 'makeplot.topology.Rd':
    \keyword{convergence,}
    \keyword{mcmc,}
    \keyword{parameter,}
    \keyword{plot,}
  File 'makeplot.treespace.Rd':
    \keyword{plot,}
    \keyword{treespace,}
  File 'print.rwty.chain.Rd':
    \keyword{MCMC,}
    \keyword{awty,}
    \keyword{convergence,}
    \keyword{phylogenetics,}
    \keyword{plot,}
  File 'slide.freq.Rd':
    \keyword{MCMC,}
    \keyword{frequency,}
  File 'topological.approx.ess.Rd':
    \keyword{distance,}
    \keyword{treespace,}
  File 'topological.autocorr.Rd':
    \keyword{autocorrelation,}
  File 'topological.pseudo.ess.Rd':
    \keyword{distance,}
    \keyword{treespace,}
  File 'treespace.Rd':
    \keyword{mds,}
    \keyword{treespace,}
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'rwty' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'acsf.cumulative.png' 'acsf.sliding.png' 'asdsf.plot.png'
  'asdsf.tree.png' 'autocorr.plot.png' 'compare.plot.png'
  'cumulative.asdsf.png' 'cumulative.posterior.png'
  'cumulative.single.png' 'ess.plot.png' 'heatmap.png' 'heatmap2.png'
  'lnl.plot.png' 'param.correlations.default.png'
  'param.correlations.supplied.png' 'param.density.plot.png'
  'param.plot.png' 'param.trace.plot.png' 'plot-comparisons.R'
  'plot-comparisons.Rmd' 'pointsplot.png' 'pointsplot2.png' 'rwty.R'
  'rwty.Rmd' 'sliding.posterior.png' 'sliding.single.png'
  'splitfreq.matrix.png' 'splitfreqs.cumulative.png'
  'splitfreqs.sliding.png' 'topology.density.plot.png'
  'topology.plot.png' 'topology.trace.plot.png'
* checking examples ... [11s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  'plot-comparisons.Rmd'
  'rwty.Rmd'
* checking re-building of vignette outputs ... [450s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE